Using high-resolution stacks of precursors to the seismic phase SS, we investigated seismic discontinuities associated with mineralogical phase changes approximately 410 and 660 kilometers (km) deep within Earth beneath South America and the surrounding oceans. Detailed maps of phase boundary topography revealed deep 410- and 660-km discontinuities in the down-dip direction of subduction, inconsistent with purely isochemical olivine phase transformation in response to lowered temperatures. Mechanisms invoking chemical heterogeneity within the mantle transition zone were explored to explain this feature. In some regions, multiple reflections from the discontinuities were detected, consistent with partial melt near 410-km depth and/or additional phase changes near 660-km depth. Thus, the origin of upper mantle heterogeneity has both chemical and thermal contributions and is associated with deeply rooted tectonic processes.